Experiment Protocol by Markdown Example

For today's experiment we will be analyzing the following blockquote:

...the twist transcription factor binds broadly across the genome and regulates important developmental events.

What we need

To accomplish this we need three things from the following list:

• an installed aligner
• a working directory
• a set of fastq files

The mutants are summarized in the following Table:

The steps we will take are indicated in this ordrered list:

1. Create a working directory
2. write a simple alignment script
   • see the class examples
3. check the server before we run the script

We also need to write some shell code

our script might look something like:

    for f in FILES
    do
      tophat f
    done

We ran it on maple, which has 12 cores 24 cores.